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Comment: GelBuddy: Tilling gel analysis tool.
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explanations
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== Short explanation: == This page lists programs which are usefull to the field of Genomics. It is mostly software related to microarrays, genome sequencing, and whole-genome analysis. Most column names are self-explanatory. "Packaging" gives cues about the difficulty of the packaging, or indicates that the program has already been packaged. "Importance" gives cues about what to package first. That is why programs already packaged have nothing written there: it does not mean that they are not important!. "Listed on... " records whether the program is listed on the official DebianMed website. === Unsorted === |
Short explanation:
This page lists programs which are usefull to the field of Genomics. It is mostly software related to microarrays, genome sequencing, and whole-genome analysis.
Most column names are self-explanatory. "Packaging" gives cues about the difficulty of the packaging, or indicates that the program has already been packaged. "Importance" gives cues about what to package first. That is why programs already packaged have nothing written there: it does not mean that they are not important!. "Listed on... " records whether the program is listed on the official DebianMed website.
Unsorted
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
RNA mapping |
no profit, no redistribution of modified versions |
impossible? |
|
no |
|
Whole-genome alignments |
[http://mummer.sourceforge.net/ mummer] |
Artistic |
make failed |
no |
|
Comparative genomics |
GPL |
[https://www.bioinformatics.uwaterloo.ca/wiki/index.php?Lagan private repository] |
free |
no |
|
Comparatige genomics |
[http://www.microbialgenomics.org/BSR/BSR_README.txt non-free] |
Prior agreement required |
|
no |
|
Genome Browser |
[http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=34513 Generic Genome Browser] |
Artistic |
maybe not easy |
Academic ones are really expensive for commercial use |
no |
Genome Browser |
[http://omicspace.riken.jp/omicBrowse/OmicBrowseRegister.html ?OmicBrowser] |
GPL |
depends on java |
flash plugin required for use |
no |
Integrated environment |
[http://sourceforge.net/projects/gmod/ Generic Model Organism Database (GMOD)] |
Artistic |
complex |
important |
no |
Genome database |
[http://www.acedb.org/ acedb] |
(L)GPL |
maybe not easy |
some programs depend on acedb libs |
no |
Database schema |
[http://fuge.sourceforge.net/ FuGE] |
not found |
xml schema |
|
no |
Generic database framework |
[http://www.gusdb.org GUS] |
BSD |
depends on java and perl |
Used by many databases |
no |
Manipulating gff files |
[http://biowiki.org/GffTools gffTools] |
no licence |
lot of manpages to write! |
|
no |
Multiple alignments |
academic |
would depend on clustalw and fastdnaml |
|
no |
|
EST clustering |
[http://www.ii.uib.no/~ketil/bioinformatics/tools.html xsact] |
not found |
Haskell program, did not build on ppc |
|
no |
Discovery of regulatory regions |
[http://www.cs.helsinki.fi/u/kpalin/EEL/ Enhancer Element Locator] |
GPL |
depends on pytohon |
free |
no |
genomic sequence analysis tools |
[http://sourceforge.net/projects/cartwheel Cartwheel Bioinformatics Package] |
GPL+LGPL |
doesn't seem difficult |
|
no |
Genetic maps |
[http://carl.agtec.uga.edu/MapMerger/ ?MapMerger] |
no licence |
php cgi |
|
no |
Database of SAGE tags |
[http://pbil.univ-lyon1.fr/software/identitag/ identitag] |
not found |
perl and sh scripts |
|
no |
Codon usage analysis |
[http://codonw.sourceforge.net/ CodonW] |
GPL |
maybe easy |
free |
no |
Visualisation of annotations |
Not found |
Depends on gtk, xml, dbi, bioperl, ... |
|
no |
|
Gene predicion |
[http://analysis.ccgb.umn.edu/diogenes/ Diogenes] |
Not found |
./configure && make fails, but it seems easy to fix |
|
no |
Rearrangements analysis |
[http://www.cs.unm.edu/~moret/GRAPPA/ Grappa] |
GPL |
straightforward |
free |
no |
Clustering analysis (+GUI) |
[http://woldlab.caltech.edu/compClust/ compClust] |
[http://woldlab.caltech.edu/compClust/debian_install.shtml unofficial package] |
Did not check if the license is DFSG-free... |
no |
|
Database clustering |
[http://bioinformatics.org/cd-hit/ CD-HIT] |
Not found, but homepage says open source |
Straighytforward |
|
no |
cis-regulatory element analysis |
[http://cistematic.caltech.edu/ cistematic] |
MIT |
depends on python and sqlite |
free |
no |
Gel analysis |
[http://www.proweb.org/gelbuddy ?GelBuddy] |
[http://www.proweb.org/gelbuddy/download.html Academic with invariant sections] |
Depends on java |
Will not be packaged unless requested |
no |
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Microarrays
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Suite |
[http://www.tm4.org/ TM4] |
artistic |
depends on java |
free |
no |
Microarrays |
[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1540 SNOMAD] |
GPL |
depends on R |
free |
no |
Microarrays |
[http://genopolis.btbs.unimib.it/genopolis/material/mattia/private_mattia.htm amda] |
GPL |
R package depending on bioconductor |
free |
no |
Image analysis for microarrays |
GPL |
depends on Qt, FFTW |
free |
no |
|
Microarrays |
[http://db.systemsbiology.net/software/VERAandSAM/ Vera, Sam] |
not found |
looks easy |
|
no |
Normalisation |
[http://www.transcriptome.ens.fr/goulphar/ Goulphar] |
GPL |
R module depending on Bioconductor |
free |
no |
Genome-scale oligonucleotide design |
[http://berry.engin.umich.edu/oligoarray2_1/ ?OligoArray 2.1] |
GPL |
Depends on Java |
free |
no |
False Discovery Rate |
[http://www.stjuderesearch.org/depts/biostats/fdrlibrary/index.html FDRlibrary] |
not found |
R library |
|
no |
False Discovery Rate |
[http://www-stat.stanford.edu/~tibs/SAM/Rdist/index.html samr] |
LGPL |
R library |
free |
no |
Visualisation |
[http://jtreeview.sourceforge.net/ Java ?TreeView] |
GPL |
[http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/treeview/ unofficial] |
free or contrib ? |
yes |
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Repeats
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Repeat masking |
Not found |
[http://www.ii.uib.no/~ketil/bioinformatics/tools.html unfficial] |
|
no |
|
Repeats analysis |
[https://nbcr.sdsc.edu/euler/ ?RepeatGluer] |
Not found |
straightforward |
|
no |
Repeat finding |
[http://repeatscout.bioprojects.org/ ?RepeatScout] |
Not found |
straightforward |
|
no |
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Genome assembling
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
BAC scaffolding |
GPL |
trivial |
free |
no |
|
BAC scaffolding |
Academic |
|
|
no |
|
Base calling |
[http://www.broad.mit.edu/ftp/distribution/software/Bass/ bass] |
BSD with advertising clause |
Does not compile out of the box |
|
no |
Base calling |
Public domain |
Old C++ which may not be compatible with recent gcc |
free |
no |
|
Band calling |
unknown |
did not find the sources |
|
no |
|
Assembling |
[http://sourceforge.net/projects/wgs-assembler/ Whole Genome Assembler] |
GPL |
|
free |
no |
Clustering
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Clustering of SAGE expression |
[http://www.bcgsc.ca/bioinfo/ge/treebuilder/ TreeBuilder3D] |
GPL |
depends on java |
|
no |
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